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Genome-wide SNPs reveal fine-scale population structure of Laodelphax striatellus in China using double-digest restriction site-associated DNA sequencing
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  • Xingya Wang,
  • Bin Lu,
  • Lingyun Shao,
  • Abid Ali,
  • Fengquan Yu,
  • Mei Yang,
  • Lei Han,
  • fuyu Sun
Xingya Wang
College of Plant Protection
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Bin Lu
Chengdu Institute of Biology, Chinese Academy of Science
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Lingyun Shao
Institute of Plant Protection
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Abid Ali
College of Life Sciences
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Fengquan Yu
Institute of Plant Protection
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Mei Yang
Institute of Plant Protection
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Lei Han
Institute of Plant Protection
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fuyu Sun
Institute of Plant Protection
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Abstract

The small brown planthopper (SBPH), Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae) is a most destructive rice pest which has caused serious economic losses in China. To effectively manage this pest, we investigated genomic polymorphism, evaluated genetic divergence and populations genetic structure of SBPH at 31 sampling sites in China using a population genomics approach. In this study, we generated over 2,813,221,369 high-quality paired-end reads (413,689.55 Mb) across 306 individuals derived from double-digest restriction site-associated DNA sequencing (ddRAD-seq), and 1925 reliable single nucleotides (SNPs) were detected with an average sequencing depth of 13.99×. Overall, low levels of genetic diversity and strong genetic differentiation among all of populations were obtained (Global FST = 0.261). Neighbour-joining dendrograms, Bayesian clustering methods, discriminant analysis of principal components (DAPC) and principal component analysis (PCA) revealed three genetically distinct groups: Southwestern group, Northern group and Eastern group. Furthermore, we also observed a high degree of admixture, widespread hybridization and gene flow among populations of Northern China. A Mantel test indicated a pattern of isolation-by-distance throughout China (r = 0.211, P = 0.031). Neutrality test indicated SBPH has experienced a recent population expansion. Accordingly, our results provide new insights into the genetics of SBPH and thus contribute to develop effective management strategies for this pest.

Peer review status:POSTED

06 Jun 2020Submitted to Ecology and Evolution
06 Jun 2020Assigned to Editor
06 Jun 2020Submission Checks Completed